Not sure what you're talking about, small proteins are evolutionarily recent additions to the repertoires of molecules. Moreover, proteins that are part of metallomes such as the proteins harboring single metal atoms are relatively recent, especially the Zinc fingers [see paper by Dupont et al. PNAS 107: 10567 (2010)], which are gene regulatory factors that act very specifically on DNA.

There is a model that is supported by phylogenomic data on how modern biochemistry proceeded in evolution and in the model ran associated with proteins appears quite late in evolution well after metabolic protein enzymes.

I'm not sure what you are talking about. The article you cite is talking about how much MORE metaloenzymes existed in eukarotes than their ancestors.

So they were there.

But whatever.

--------------Ignored by those who can't provide evidence for their claims.